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Literature summary for 2.4.2.1 extracted from

  • Narczyk, M.; Bertosa, B.; Papa, L.; Vukovic, V.; Lescic Asler, I.; Wielgus-Kutrowska, B.; Bzowska, A.; Luic, M.; Stefanic, Z.
    Helicobacterpylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features (2018), FEBS J., 285, 1305-1325 .
    View publication on PubMed
Search for more literature for 2.4.2.1

Cloned(Commentary)

Cloned (Comment) Organism
gene deoD, recombinant expression of the enzyme in Escherichia coli cell strain BL21-CodonPlus(DE3)-RIL Helicobacter pylori

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant enzyme in apoform and in complex with phosphate and with formycin A as binary and ternary complexes, X-ray diffraction structure determination and analysis Helicobacter pylori

Inhibitors

Inhibitors Comment Organism Structure
Formycin A
-
 Helicobacter pylori

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
 additional information kinetic analysis, HpPNP has low affinity towards the natural substrate adenosine Helicobacter pylori
0.0031 0.0056 phosphate pH 7.0, 25°C, with 7-methylguanosine Helicobacter pylori
0.0193
-
 guanosine pH 7.0, 25°C Helicobacter pylori
0.0544
-
 7-methylguanosine pH 7.0, 25°C Helicobacter pylori
0.126
-
 phosphate pH 7.0, 25°C, with guanosine Helicobacter pylori

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ Mg2+ ions cause a marked increase in the apparent Michaelis constants for phosphate, hence also most probably an increase in the dissociation constant of phosphate-enzyme complex Helicobacter pylori

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
7-methylguanosine + phosphate Helicobacter pylori
-
 7-methylguanine + alpha-D-ribose 1-phosphate
-
 r
7-methylguanosine + phosphate Helicobacter pylori ATCC 700392
-
 7-methylguanine + alpha-D-ribose 1-phosphate
-
 r
7-methylguanosine + phosphate Helicobacter pylori 26695
-
 7-methylguanine + alpha-D-ribose 1-phosphate
-
 r
adenosine + phosphate Helicobacter pylori low activity adenine + alpha-D-ribose 1-phosphate
-
 r
adenosine + phosphate Helicobacter pylori ATCC 700392 low activity adenine + alpha-D-ribose 1-phosphate
-
 r
adenosine + phosphate Helicobacter pylori 26695 low activity adenine + alpha-D-ribose 1-phosphate
-
 r
guanosine + phosphate Helicobacter pylori
-
 guanine + alpha-D-ribose 1-phosphate
-
 r
guanosine + phosphate Helicobacter pylori ATCC 700392
-
 guanine + alpha-D-ribose 1-phosphate
-
 r
guanosine + phosphate Helicobacter pylori 26695
-
 guanine + alpha-D-ribose 1-phosphate
-
 r
inosine + phosphate Helicobacter pylori
-
 hypoxanthine + alpha-D-ribose 1-phosphate
-
 r
inosine + phosphate Helicobacter pylori ATCC 700392
-
 hypoxanthine + alpha-D-ribose 1-phosphate
-
 r
inosine + phosphate Helicobacter pylori 26695
-
 hypoxanthine + alpha-D-ribose 1-phosphate
-
 r

Organism

Organism UniProt Comment Textmining
Helicobacter pylori P56463 multifunctional fusion protein
-
Helicobacter pylori 26695 P56463 multifunctional fusion protein
-
Helicobacter pylori ATCC 700392 P56463 multifunctional fusion protein
-

Purification (Commentary)

Purification (Comment) Organism
recombinant enzyme by anion exchange chromatography followed by affinity chromatography Helicobacter pylori

Reaction

Reaction Comment Organism Reaction ID
purine ribonucleoside + phosphate = purine + alpha-D-ribose 1-phosphate the protonation of the purine base at position N(7) by the side chain of Asp204 is the first step in the catalytic cleavage of the glycosidic bond Helicobacter pylori
a

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
6
-
 purified enzyme, pH 7.0, 25°C, substrates adenosine and phosphate Helicobacter pylori
9.8
-
 purified enzyme, pH 7.0, 25°C, substrates 7-methylguanosine and phosphate Helicobacter pylori
13.8
-
 purified enzyme, pH 7.0, 25°C, substrates guanosine and phosphate Helicobacter pylori
49.4
-
 purified enzyme, pH 7.0, 25°C, substrates inosine and phosphate Helicobacter pylori

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
7-methylguanosine + phosphate
-
 Helicobacter pylori 7-methylguanine + alpha-D-ribose 1-phosphate
-
 r
7-methylguanosine + phosphate
-
 Helicobacter pylori ATCC 700392 7-methylguanine + alpha-D-ribose 1-phosphate
-
 r
7-methylguanosine + phosphate
-
 Helicobacter pylori 26695 7-methylguanine + alpha-D-ribose 1-phosphate
-
 r
adenosine + phosphate low activity Helicobacter pylori adenine + alpha-D-ribose 1-phosphate
-
 r
adenosine + phosphate low activity Helicobacter pylori ATCC 700392 adenine + alpha-D-ribose 1-phosphate
-
 r
adenosine + phosphate low activity Helicobacter pylori 26695 adenine + alpha-D-ribose 1-phosphate
-
 r
guanosine + phosphate
-
 Helicobacter pylori guanine + alpha-D-ribose 1-phosphate
-
 r
guanosine + phosphate
-
 Helicobacter pylori ATCC 700392 guanine + alpha-D-ribose 1-phosphate
-
 r
guanosine + phosphate
-
 Helicobacter pylori 26695 guanine + alpha-D-ribose 1-phosphate
-
 r
inosine + phosphate
-
 Helicobacter pylori hypoxanthine + alpha-D-ribose 1-phosphate
-
 r
inosine + phosphate best substrate Helicobacter pylori hypoxanthine + alpha-D-ribose 1-phosphate
-
 r
inosine + phosphate
-
 Helicobacter pylori ATCC 700392 hypoxanthine + alpha-D-ribose 1-phosphate
-
 r
inosine + phosphate best substrate Helicobacter pylori ATCC 700392 hypoxanthine + alpha-D-ribose 1-phosphate
-
 r
inosine + phosphate
-
 Helicobacter pylori 26695 hypoxanthine + alpha-D-ribose 1-phosphate
-
 r
inosine + phosphate best substrate Helicobacter pylori 26695 hypoxanthine + alpha-D-ribose 1-phosphate
-
 r

Subunits

Subunits Comment Organism
homohexamer
-
 Helicobacter pylori

Synonyms

Synonyms Comment Organism
DeoD
-
 Helicobacter pylori
HpPNP
-
 Helicobacter pylori
PNP
-
 Helicobacter pylori

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
25
-
 assay at Helicobacter pylori

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7
-
 assay at Helicobacter pylori

pH Stability

pH Stability pH Stability Maximum Comment Organism
6 10 purified enzyme, 25°C, 90% activity remaining Helicobacter pylori

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
additional information
-
 additional information inhibition kinetics Helicobacter pylori
0.014
-
 Formycin A pH 7.0, 25°C Helicobacter pylori

General Information

General Information Comment Organism
additional information enzyme kinetics, ligand binding, docking, and molecular dynamics simulation studies, overview. Active site structure and ligand binding structure analysis. HpPNP has low affinity towards the natural substrate adenosine. Molecular dynamics simulations show that Pi moves out of most active sites, in accordance with its weak binding. Conformational changes between nonstandard and standard binding modes of nucleoside are observed during the simulations. The protonation of the purine base at position N(7) by the side chain of Asp204 is the first step in the catalytic cleavage of the glycosidic bond. Hence, 7-methylguanosine bears one feature of the transition state and does not need to be protonated Helicobacter pylori